This is usually accompanied by more general interactions with the surface of the DNA molecule, which may simply stabilize the DNA-protein complex.

examples of specific DNA-binding motifs

helix–turn–helix (HTH) motif

zinc finger motif

Leucine zippers

The contacts formed between DNA and its binding proteins are __

non-covalent

DNA binding proteins interact with the chemical elements in the __

major groove (sometimes also minor groove)

To maximize contacts and specificity, many DNA-binding proteins are __

dimers

helix-turn-helix motif

Two α-helices separated by a turn (known as β-turn)

The second α-helix (recognition helix) is on the surface of the protein in an orientation that enables it to fit inside the major groove of a DNA molecule (e.g. lactose repressor).

For contact between DNA and proteins, the __ should be complementary to the chemical elements of base pairs.

shape

polarity

hydrogen donor and acceptor properties of the R groups of the amino acids of the protein

In the case of __ base pairs, hydrophobic interactions are also important.

A:T and T:A

On the surface of the DNA helix there are __ interactions between __

electrostatic;

negative charges on the phosphate and positive charges on the R groups of amino acids such as lysine and arginine

In an helix-turn-helix motif with DNA, __ are made between one α-helix and the DNA backbone and also bonds formed between the __

hydrogen bonds & salt bridges;

recognition α-helix & major groove of DNA chemical elements

examples of the R chains of amino acids interacting with major groove chemical elements

T:A and C:G

Cys2His2 finger

a type of zinc finger protein: The zinc atom is held between 2 cysteines within the β-sheet of the motif and 2 histidines in the α-helix

The a-helix is the part of the motif that

makes contacts within the major groove.

Proteins interact with other proteins by:

interaction between the pre-folded domains

new folding upon interaction of 2 proteins

change in configuration or folding upon modifications such as phosphorylation or acetylation

The protein 3D structure and RNA 3D structure can interact in specific manners such as:

interaction of each tRNA with the specific enzyme that specifically links the correct amino acid to the correct tRNA

Alternatively in other cases, it is possible that interaction of protein and RNA causes or stabilizes their folding.

Almost all the processes in the cell from DNA and RNA polymerization to metabolism and generation and use of energy is accelerated by the activity of the __ as the biological catalysts.

enzymes

enzyme facts

required in small amounts

not altered/consumed in rxn (or returned to their original status after the rxn)

no effect on thermodynamics of rxn (does not supply E or determine product/reactants ratio)

do accelerate rate of reaction (kinetics)

highly specific for substrate/reactant

very few side reactions (i.e. very "clean")

subject to regulation

To start any reaction, a __ is needed to push the molecules to the active state. Then if the reaction is accompanied with the __, it will go forward.

small activation energy (EA);

release of energy

An enzyme __ EA. This is usually done by the __ of enzymes.

lowers (so that ambient fluctuations of E are sufficient to start the reaction);

active site

A __ may interact with a domain other than the active site of the enzyme. If this interaction causes change of configuration in the protein and eventually the configuration of the active site, it may __. This type of regulating the activity of a protein is known as __

ligand;

induce or reduce the activity of the enzyme (depends on the type of change);

allosteric regulation (not regulated by the real substrate or the analog of a substrate)

example of allosteric regulation: A lac repressor (dimer protein) binds to a specific sequence of DNA.

binding of allolactose (ligand) to the Lac repressor protein → change of configuration in the protein → its detachment from the DNA sequence